Alkali cation-mediated topology displayed by an exonic G-rich sequence of TRPA1 gene

Abstract

G-rich sequences are intrinsic parts of the genome, widespread in promoters, telomeres, or other regulatory regions. The in vivo existence and biological significance have established the functional aspect of G-quadruplex structures and thus have developed immense interest in exploring their therapeutic aspects. Herein, using biophysical methods, we examined the structural status and comprehensive cation-dependence of a 17-bp G-rich genomic sequence (SKGT17) located in the coding region of the human TRPA1 gene, known to be associated with various neurovascular, cardiovascular, and respiratory conditions. TRPA1 is primarily seen as a therapeutic target for the development of novel analgesics. Bioinformatics analysis has suggested that 17-bp quadruplex motif is a binding site for transcription factor 'Sp1'. The formation and recognition of SKGT17 G-quadruplex might impact its regulatory functioning. Biophysical studies confirmed that the presence of alkali metal ions facilitated the formation of G-quadruplex in parallel topology. Native gel further substantiated the formation of a biomolecular species. Circular dichroism (CD), UV-thermal melting (Tm), and CD melting confirmed the formation of parallel G-quadruplex with metal ion-dependent stability. The stability of the G-quadruplex formed is found to be significantly high in the presence of K⁺ ions than that of other ions. Intriguingly, we have also established that this segment of the TRAP1 gene favors G-quadruplex formation over its participation in the corresponding duplex formation under K⁺ ions conditions. This study attempts to explain the rationale for the stabilization of G-quadruplex in the presence of alkali metal ions and may add to a better understanding and insights into DNA-metal ions interactions.

Communicated by Ramaswamy H. Sarma

Keywords:

• G-quadruplex
• TRPA1 gene
• alkali metal ions
• circular dichroism
• CD melting
• UV–vis thermal melting
• native gel electrophoresis

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This research received Faculty Research Programme Grant (IOE/FRP-PCMS/2020/27) from the University of Delhi, Delhi, and Shoaib would like to acknowledge the University Grants Commission (UGC) for the JRF & SRF support.